phyl.vcv: Compute evolutionary VCV matrix for a tree & dataset

Description Usage Arguments Details Value Author(s) References

View source: R/utilities.R

Description

Primarily an internal function for phyl.pca; this can be used to compute the phylogenetic trait variance-covariance matrix given a phylogenetic VCV, lambda, and a data matrix. Should not be confused with vcv.phylo in the "ape" package (although one of the objects returned is the output of vcv.phylo).

Usage

1
phyl.vcv(X, C, lambda)

Arguments

lambda

value for λ transformation.

X

data matrix.

C

matrix containing the height above the root of each pair of species in the tree. Typically this will have been produced by calling vcv.phylo.

Details

Do not use unless you know what you're doing.

Value

A list containing three elements, as follows: C, the matrix vcv.phylo transformed by lambda; R, the among trait variance-covariance matrix for the data in X; and alpha, a vector of ancestral states at the root node of the tree.

Author(s)

Liam Revell [email protected]

References

Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.


liamrevell/phytools documentation built on Nov. 22, 2018, 5:21 p.m.